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Genome evolution and evolutionary systems biology

Section edited by Maria Anisimova, Arndt von Haeseler and David Liberles

This section considers studies on genome evolution and systems biology approaches to determining evolutionary processes.

Page 4 of 8

  1. Content type: Research article

    The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless ...

    Authors: Leon Huynen, Takayuki Suzuki, Toshihiko Ogura, Yusuke Watanabe, Craig D Millar, Michael Hofreiter, Craig Smith, Sara Mirmoeini and David M Lambert

    Citation: BMC Evolutionary Biology 2014 14:75

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  2. Content type: Research article

    Phenylalanine ammonia-lyase (PAL; E.C.4.3.1.5) is a key enzyme of the phenylpropanoid pathway in plant development, and it catalyses the deamination of phenylalanine to trans-cinnamic acid, leading to the prod...

    Authors: Zhihua Wu, Songtao Gui, Shuzhen Wang and Yi Ding

    Citation: BMC Evolutionary Biology 2014 14:100

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  3. Content type: Research article

    Synonymous codon usage can affect many cellular processes, particularly those associated with translation such as polypeptide elongation and folding, mRNA degradation/stability, and splicing. Highly expressed ...

    Authors: Jingjing Du, Sarah Z Dungan, Amir Sabouhanian and Belinda SW Chang

    Citation: BMC Evolutionary Biology 2014 14:96

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  4. Content type: Research article

    Many studies have found functional RNA secondary structures are selectively conserved among species. But, the effect of RNA structure selection on coding sequence evolution remains unknown. To address this pro...

    Authors: Wanjun Gu, Musheng Li, Yuming Xu, Ting Wang, Jae-Hong Ko and Tong Zhou

    Citation: BMC Evolutionary Biology 2014 14:87

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  5. Content type: Research article

    Reactive carbonyl species (RCS), such as methylglyoxal (MG) and glyoxal (GO), are synthesized as toxic metabolites in living systems. Mechanisms of RCS detoxification include the glutathione (GSH)-dependent sy...

    Authors: Qiaoqiao Zhao, Yang Su, Zhikang Wang, Caiping Chen, Tongsiyu Wu and Ying Huang

    Citation: BMC Evolutionary Biology 2014 14:86

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  6. Content type: Research article

    miRNAs are a major class of regulators of gene expression in metazoans. By targeting cognate mRNAs, miRNAs are involved in regulating most, if not all, biological processes in different cell and tissue types. ...

    Authors: Hossein Zare, Arkady Khodursky and Vittorio Sartorelli

    Citation: BMC Evolutionary Biology 2014 14:74

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  7. Content type: Research article

    Horizontal gene transfer (HGT) has been suggested as the mechanism by which various plant parasitic nematode species have obtained genes important in parasitism. In particular, cellulase genes have been acquir...

    Authors: Juan E Palomares-Rius, Yuuri Hirooka, Isheng J Tsai, Hayato Masuya, Akina Hino, Natsumi Kanzaki, John T Jones and Taisei Kikuchi

    Citation: BMC Evolutionary Biology 2014 14:69

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  8. Content type: Research article

    Cytochrome P450 CYP2C19 metabolizes a wide range of pharmacologically active substances and a relatively small number of naturally occurring environmental toxins. Poor activity alleles of CYP2C19 are very frequen...

    Authors: Ramatoulie E Janha, Archibald Worwui, Kenneth J Linton, Seif O Shaheen, Fatoumatta Sisay-Joof and Robert T Walton

    Citation: BMC Evolutionary Biology 2014 14:71

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  9. Content type: Research article

    Debate continues as to whether allopatric speciation or peripatric speciation through a founder effect is the predominant force driving evolution in vertebrates. The mouse lemurs of Madagascar are a system in ...

    Authors: Christopher Blair, Kellie L Heckman, Amy L Russell and Anne D Yoder

    Citation: BMC Evolutionary Biology 2014 14:57

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  10. Content type: Research article

    Functionality of the tetrameric hemoglobin molecule seems to be determined by a few amino acids located in key positions. Oxygen binding encompasses structural changes at the interfaces between the α1β2 and α2...

    Authors: Øivind Andersen, Maria Cristina De Rosa, Prakash Yadav, Davide Pirolli, Jorge MO Fernandes, Paul R Berg, Sissel Jentoft and Carl Andrè

    Citation: BMC Evolutionary Biology 2014 14:54

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  11. Content type: Research article

    The oriental fruit fly, Bactrocera dorsalis s.s., is one of the most important quarantine pests in many countries, including China. Although the oriental fruit fly has been investigated extensively, its origins a...

    Authors: Zhong-Zhen Wu, Hong-Mei Li, Shu-Ying Bin, Jun Ma, Hua-Liang He, Xian-Feng Li, Fei-Liang Gong and Jin-Tian Lin

    Citation: BMC Evolutionary Biology 2014 14:55

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  12. Content type: Research article

    Pollen donor compositions differ during the early stages of reproduction due to various selection mechanisms. In addition, ovules linearly ordered within a fruit have different probabilities of reaching maturi...

    Authors: Cun-Quan Yuan, Yu-Han Sun, Yun-Fei Li, Ke-Qi Zhao, Rui-Yang Hu and Yun Li

    Citation: BMC Evolutionary Biology 2014 14:53

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  13. Content type: Research article

    The existence of introns in eukaryotic genes is believed to provide an evolutionary advantage by increasing protein diversity through exon shuffling and alternative splicing. However, this eukaryotic feature i...

    Authors: Olga Gorlova, Alexey Fedorov, Christopher Logothetis, Christopher Amos and Ivan Gorlov

    Citation: BMC Evolutionary Biology 2014 14:50

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  14. Content type: Research article

    Poecilimon and Isophya are the largest genera of the tribe Barbitistini and among the most systematically complicated and evolutionarily intriguing groups of Palearctic tettigoniids. We examined the genomic organ...

    Authors: Beata Grzywacz, Dragan P Chobanov, Anna Maryańska-Nadachowska, Tatyana V Karamysheva, Klaus-Gerhard Heller and Elżbieta Warchałowska-Śliwa

    Citation: BMC Evolutionary Biology 2014 14:48

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  15. Content type: Research article

    The GTPase eEF1A is the eukaryotic factor responsible for the essential, universal function of aminoacyl-tRNA delivery to the ribosome. Surprisingly, eEF1A is not universally present in eukaryotes, being repla...

    Authors: Gemma C Atkinson, Anton Kuzmenko, Ivan Chicherin, Axel Soosaar, Tanel Tenson, Martin Carr, Piotr Kamenski and Vasili Hauryliuk

    Citation: BMC Evolutionary Biology 2014 14:35

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  16. Content type: Research article

    Spider silks are spectacular examples of phenotypic diversity arising from adaptive molecular evolution. An individual spider can produce an array of specialized silks, with the majority of constituent silk pr...

    Authors: R Crystal Chaw, Yonghui Zhao, Jie Wei, Nadia A Ayoub, Ryan Allen, Kirmanj Atrushi and Cheryl Y Hayashi

    Citation: BMC Evolutionary Biology 2014 14:31

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  17. Content type: Research article

    The neuropeptide Kiss and its receptor KissR are key-actors in the brain control of reproduction in mammals, where they are responsible for the stimulation of the activity of GnRH neurones. Investigation in ot...

    Authors: Jérémy Pasquier, Anne-Gaëlle Lafont, Karine Rousseau, Bruno Quérat, Philippe Chemineau and Sylvie Dufour

    Citation: BMC Evolutionary Biology 2014 14:30

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  18. Content type: Research article

    Methionine adenosyltransferase (MAT) is a ubiquitous essential enzyme that, in eukaryotes, occurs in two relatively divergent paralogues: MAT and MATX. MATX has a punctate distribution across the tree of eukar...

    Authors: Jana Szabová, Naoji Yubuki, Brian S Leander, Richard E Triemer and Vladimír Hampl

    Citation: BMC Evolutionary Biology 2014 14:25

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  19. Content type: Research article

    Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the ...

    Authors: Han Ming Gan, Mark B Schultz and Christopher M Austin

    Citation: BMC Evolutionary Biology 2014 14:19

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  20. Content type: Research article

    The recent availability of sequenced genomes from a broad array of chordates (cephalochordates, urochordates and vertebrates) has allowed us to systematically analyze the evolution of uroplakins: tetraspanins ...

    Authors: Rob DeSalle, Javier U Chicote, Tung-Tien Sun and Antonio Garcia-España

    Citation: BMC Evolutionary Biology 2014 14:13

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  21. Content type: Research article

    Nitrogen uptake, reallocation within the plant, and between subcellular compartments involves ammonium, nitrate and peptide transporters. Ammonium transporters are separated into two distinct families (AMT1 an...

    Authors: Neil JJB von Wittgenstein, Cuong H Le, Barbara J Hawkins and Jürgen Ehlting

    Citation: BMC Evolutionary Biology 2014 14:11

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  22. Content type: Research article

    The molecular history of animal evolution from single-celled ancestors remains a major question in biology, and little is known regarding the evolution of cell cycle regulation during animal emergence. In this...

    Authors: Lihuan Cao, Fang Chen, Xianmei Yang, Weijin Xu, Jun Xie and Long Yu

    Citation: BMC Evolutionary Biology 2014 14:10

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  23. Content type: Research article

    Ticks are blood-sucking arthropods and a primary function of tick salivary proteins is to counteract the host’s immune response. Tick salivary Kunitz-domain proteins perform multiple functions within the feedi...

    Authors: Alexandra Schwarz, Alejandro Cabezas-Cruz, Jan Kopecký and James J Valdés

    Citation: BMC Evolutionary Biology 2014 14:4

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  24. Content type: Research article

    New World leaf-nosed bats, Phyllostomidae, represent a lineage of Chiroptera marked by unprecedented morphological/ecological diversity and extensive intergeneric chromosomal reorganization. There are still di...

    Authors: Cibele G Sotero-Caio, Marianne Volleth, Lauren S Gollahon, Beiyuan Fu, William Cheng, Bee L Ng, Fengtang Yang and Robert J Baker

    Citation: BMC Evolutionary Biology 2013 13:276

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  25. Content type: Research article

    Fatty acids, a considerable fraction of lipid molecules, participate in fundamental physiological processes. They undergo activation into their corresponding CoA esters for oxidation or esterification into com...

    Authors: Mónica Lopes-Marques, Isabel Cunha, Maria Armanda Reis-Henriques, Miguel M Santos and L Filipe C Castro

    Citation: BMC Evolutionary Biology 2013 13:271

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  26. Content type: Research article

    Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. However, the origin and evolution of most plasmids remains unclear, especially for megaplasmids. Strain...

    Authors: Jinshui Zheng, Donghai Peng, Lifang Ruan and Ming Sun

    Citation: BMC Evolutionary Biology 2013 13:262

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  27. Content type: Research article

    Classical major histocompatibility complex (MHC) class II molecules play an essential role in presenting peptide antigens to CD4+ T lymphocytes in the acquired immune system. The non-classical class II DM molecul...

    Authors: Johannes M Dijkstra, Unni Grimholt, Jong Leong, Ben F Koop and Keiichiro Hashimoto

    Citation: BMC Evolutionary Biology 2013 13:260

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  28. Content type: Research article

    The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and...

    Authors: Janine E Deakin, Margaret L Delbridge, Edda Koina, Nerida Harley, Amber E Alsop, Chenwei Wang, Vidushi S Patel and Jennifer A Marshall Graves

    Citation: BMC Evolutionary Biology 2013 13:258

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  29. Content type: Research article

    Hypodontus macropi is a common intestinal nematode of a range of kangaroos and wallabies (macropodid marsupials). Based on previous multilocus enzyme electrophoresis (MEE) and nuclear ribosomal DNA sequence data ...

    Authors: Abdul Jabbar, Ian Beveridge, Namitha Mohandas, Neil B Chilton, D Timothy J Littlewood, Aaron R Jex and Robin B Gasser

    Citation: BMC Evolutionary Biology 2013 13:259

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  30. Content type: Research article

    Placental mammals display a huge range of life history traits, including size, longevity, metabolic rate and germ line generation time. Although a number of general trends have been proposed between these trai...

    Authors: Claire C Morgan, Ann M Mc Cartney, Mark TA Donoghue, Noeleen B Loughran, Charles Spillane, Emma C Teeling and Mary J O’Connell

    Citation: BMC Evolutionary Biology 2013 13:251

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  31. Content type: Research article

    Many long non-coding RNA (lncRNA) genes identified in mammals have multiple exons and functional domains, allowing them to bind to polycomb proteins, DNA methyltransferases, and specific DNA sequences to regul...

    Authors: Sha He, Weiling Gu, Yize Li and Hao Zhu

    Citation: BMC Evolutionary Biology 2013 13:247

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  32. Content type: Research article

    One of the most striking features of avian vision is the variation in spectral sensitivity of the short wavelength sensitive (SWS1) opsins, which can be divided into two sub-types: violet- and UV- sensitive (V...

    Authors: Ilke van Hazel, Amir Sabouhanian, Lainy Day, John A Endler and Belinda SW Chang

    Citation: BMC Evolutionary Biology 2013 13:250

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  33. Content type: Research article

    Pseudogenes are traditionally considered “dead” genes, therefore lacking biological functions. This view has however been challenged during the last decade. This is the case of the Protein phosphatase 1 regula...

    Authors: Luís Korrodi-Gregório, Joana Abrantes, Thorsten Muller, José Melo-Ferreira, Katrin Marcus, Odete AB da Cruz e Silva, Margarida Fardilha and Pedro J Esteves

    Citation: BMC Evolutionary Biology 2013 13:242

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  34. Content type: Research article

    Hydrophobins are small secreted cysteine-rich proteins that play diverse roles during different phases of fungal life cycle. In basidiomycetes, hydrophobin-encoding genes often form large multigene families wi...

    Authors: Anthony C Mgbeahuruike, Andriy Kovalchuk, Hongxin Chen, Wimal Ubhayasekera and Fred O Asiegbu

    Citation: BMC Evolutionary Biology 2013 13:240

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  35. Content type: Research article

    Vertebrate color vision is dependent on four major color opsin subtypes: RH2 (green opsin), SWS1 (ultraviolet opsin), SWS2 (blue opsin), and LWS (red opsin). Together with the dim-light receptor rhodopsin (RH1...

    Authors: David Lagman, Daniel Ocampo Daza, Jenny Widmark, Xesús M Abalo, Görel Sundström and Dan Larhammar

    Citation: BMC Evolutionary Biology 2013 13:238

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  36. Content type: Research article

    Guanine-cytosine (GC) composition is an important feature of genomes. Likewise, amino acid composition is a distinct, but less valued, feature of proteomes. A major concern is that it is not clear what valuabl...

    Authors: Wanping Chen, Yanchun Shao and Fusheng Chen

    Citation: BMC Evolutionary Biology 2013 13:219

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  37. Content type: Research article

    The glycolytic pathway is central to cellular energy production. Selection on individual enzymes within glycolysis, particularly phosphoglucose isomerase (Pgi), has been associated with metabolic performance in n...

    Authors: Luke T Dunning, Alice B Dennis, Geoffrey Thomson, Brent J Sinclair, Richard D Newcomb and Thomas R Buckley

    Citation: BMC Evolutionary Biology 2013 13:215

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  38. Content type: Research article

    Horizontal gene transfer (HGT) allows for rapid spread of genetic material between species, increasing genetic and phenotypic diversity. Although HGT contributes to adaptation and is widespread in many bacteri...

    Authors: Sara E Hester, Jihye Park, Laura L Goodfield, Heather A Feaga, Andrew Preston and Eric T Harvill

    Citation: BMC Evolutionary Biology 2013 13:209

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  39. Content type: Research article

    The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date bac...

    Authors: Stefanie Mühlhausen and Martin Kollmar

    Citation: BMC Evolutionary Biology 2013 13:202

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  40. Content type: Research article

    In vertebrates, it has been repeatedly demonstrated that genes encoding proteins involved in pathogen-recognition by adaptive immunity (e.g. MHC) are subject to intensive diversifying selection. On the other hand...

    Authors: Alena Fornůsková, Michal Vinkler, Marie Pagès, Maxime Galan, Emmanuelle Jousselin, Frederique Cerqueira, Serge Morand, Nathalie Charbonnel, Josef Bryja and Jean-François Cosson

    Citation: BMC Evolutionary Biology 2013 13:194

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  41. Content type: Research article

    Osmoregulation was a primary challenge for cetaceans during the evolutionary transition from a terrestrial to a mainly hyperosmotic environment. Several physiological mechanisms have been suggested to maintain...

    Authors: Shixia Xu, Yunxia Yang, Xuming Zhou, Junxiao Xu, Kaiya Zhou and Guang Yang

    Citation: BMC Evolutionary Biology 2013 13:189

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  42. Content type: Research article

    Trypanosomatids of the genera Angomonas and Strigomonas live in a mutualistic association characterized by extensive metabolic cooperation with obligate endosymbiotic Betaproteobacteria. However, the role played ...

    Authors: João MP Alves, Cecilia C Klein, Flávia Maia da Silva, André G Costa-Martins, Myrna G Serrano, Gregory A Buck, Ana Tereza R Vasconcelos, Marie-France Sagot, Marta MG Teixeira, Maria Cristina M Motta and Erney P Camargo

    Citation: BMC Evolutionary Biology 2013 13:190

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  43. Content type: Research article

    Pathogenicity islands (PAIs) or genomic islands (GEIs) are considered to be the result of a recent horizontal transfer. Detecting PAIs/GEIs as well as their putative source can provide insight into the organis...

    Authors: Catherine Putonti, Bogdan Nowicki, Michael Shaffer, Yuriy Fofanov and Stella Nowicki

    Citation: BMC Evolutionary Biology 2013 13:184

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  44. Content type: Research article

    Isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. In most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosp...

    Authors: Lorenzo Carretero-Paulet, Agnieszka Lipska, Jordi Pérez-Gil, Félix J Sangari, Victor A Albert and Manuel Rodríguez-Concepción

    Citation: BMC Evolutionary Biology 2013 13:180

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2017 Journal Metrics

  • Citation Impact
    3.027 - 2-year Impact Factor
    3.628 - 5-year Impact Factor
    1.16 - Source Normalized Impact per Paper (SNIP)
    1.656 - SCImago Journal Rank (SJR)

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